Is MAP1B p.Pro1036= (c.3108G>A) pathogenic?

MAP1B p.Pro1036= (c.3108G>A) is classified Likely benign in MAP1B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-05-30). Ultra-rare (popmax 0.0164%, mid); Associated with MAP1B-related disorder.

What condition is associated with MAP1B p.Pro1036= (c.3108G>A)?

MAP1B p.Pro1036= (c.3108G>A) is associated with MAP1B-related disorder (ClinVar).

How common is MAP1B p.Pro1036= (c.3108G>A) in the general population?

MAP1B p.Pro1036= (c.3108G>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

MAP1B p.Pro1036=

c.3108G>A · rs150527364 · VCV3046248

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

MAP1B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -16	GERP -4.4
Overall
CADD	0.08	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,080 alleles

Filtering AF 0.00662% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00498%

Overall 0.00961% 155/1,613,600 alleles · ultra-rare exomes 141/1,461,564 · genomes 14/152,036 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.122%	822
Remaining individualsnot grpmax-eligible	0.0192%	5,207
Middle Easterngrpmax	0.0164%	6,080
Admixed American	0.0133%	7,499
African / African-American	0.0107%	9,356
South Asian	0.00769%	13,010
European (non-Finnish)	0.00661%	15,128
Finnishnot grpmax-eligible	0.00628%	15,924
East Asian	0.00223%	44,888

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAP1B
Protein: p.Pro1036=
Coding: c.3108G>A
MANE Select: NM_005909
dbSNP: rs150527364
Type: single nucleotide variant
Location: chr5:72196463 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18
Residue 1036: the 'disordered' region; a UniProt-annotated variant site (in pvnh9); a UniProt-annotated variant site (in pvnh9; no effect on protein expression)

Full MAP1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MAP1B-related disorder

Similar variants

MAP1B p.Pro1036Thr Uncertain significance ★ ⚠ same residue
MAP1B p.Pro1036Leu Likely benign ★ same residue
MAP1B p.Pro1182Arg Uncertain significance ★★ ⚠ same condition
MAP1B p.Thr2194Met Uncertain significance ★★ ⚠ same condition
MAP1B p.Gln325Ter Likely pathogenic ★ same condition
MAP1B p.Lys751Ter Likely pathogenic ★ same condition
MAP1B p.Arg64Gln Uncertain significance ★ same condition
MAP1B p.Asp1637Asn Uncertain significance ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/map1b-p-pro1036 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown